January 26, 2018

What is R Markdown

  • R Markdown is a file format for making dynamic documents with R
    • A mix text and R code together in one document
    • Knit the document = execute code and compile the document
    • A text file that can be tracked by git
    • User-friendly (compared to LaTeX) but still powerful
  • Written in markdown, but can include HTML, LaTeX and R code

What is R Markdown

Why R Markdown?

  1. Reproducable research
    • Mouse clicking is not reproducable
    • Copying and pasting R output from text files to documents is not reproducable

You when you start your project:

Why R Markdown?

  1. Reproducable research
    • Mouse clicking is not reproducable
    • Copying and pasting R output from text files to documents is not reproducable
After getting the second round of revisions back:

Why R Markdown?

  1. Reproducable research
    • Mouse clicking is not reproducable
    • Copying and pasting R output from text files to documents is not reproducable
    • A work flow that forces me to make things more reproducable


Why R Markdown?

  1. Version control
    • text file that can be tracked by git

Why R Markdown?

  1. Version control
    • text file that can be tracked by git
    • this is embarrassing

"

Why this work flow?

  • One of many possible work flows to achieve those goals - knitr, sweave, latex with a master script
    • Anything to avoid clicking the mouse
  • Choose whatever works for you!


Why this work flow?

  • rmarkdown is:
    • easy to learn with lots of support from RStudio
    • able to include LaTeX or HTML code
    • creates PDF and HTML output (and Word)
    • keep the tex file for journal submission

Some things could be better

  • including journal templates
  • this cats jumping skills

Cool features

  • Everything is in one document
  • Call external scripts
  • Caching
  • Make PDF or HTML presentations (beamer, isolides, slidy)
  • Easy to include:
    • references
    • equations
    • lists
    • figures
    • cross-references
    • tables
    • actual r code